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BMRB: 50088

Structure and function of the bacterial toxin phenomycin

Authors

Assembly

Phenomycin

Entity

1. Phenomycin (polymer, Thiol state: not present), 93 monomers, 9854.012 Da Detail

GAMANPKTIK AAAYNQARST LADAGSRTAA KSHPIHGKTD VPVSYGTSLL AAARDEFRQA DKKLPAKDKK SDMSIAHYNA VHSAAKTMGI DTW

Formula weight

9854.012 Da

Source organism

Streptomyces roseoverticillatus

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.0 %, Completeness (bb): 98.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.0 % (984 of 1014)	96.7 % (506 of 523)	97.0 % (384 of 396)	98.9 % (94 of 95)
Backbone	98.7 % (543 of 550)	98.4 % (184 of 187)	98.9 % (271 of 274)	98.9 % (88 of 89)
Sidechain	95.7 % (528 of 552)	95.8 % (322 of 336)	95.2 % (200 of 210)	100.0 % (6 of 6)
Aromatic	79.0 % (49 of 62)	80.6 % (25 of 31)	76.7 % (23 of 30)	100.0 % (1 of 1)
Methyl	100.0 % (96 of 96)	100.0 % (48 of 48)	100.0 % (48 of 48)

1. Phenomycin

GAMANPKTIK AAAYNQARST LADAGSRTAA KSHPIHGKTD VPVSYGTSLL AAARDEFRQA DKKLPAKDKK SDMSIAHYNA VHSAAKTMGI DTW

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

LACS Plot; CA

Referencing offset: 0.43 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.43 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.08 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.07 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6TKT, Strand ID: A Detail

Release date

2019-11-14

Citation

Structure and Function of the Bacterial Protein Toxin Phenomycin
Hansen, B.K., Larsen, C.K., Nielsen, J.T., Svenningsen, E.B., Van, L.B., Jacobsen, K.M., Bjerring, M., Flygaard, R.K., Jenner, L.B., Nejsum, L.N., Brodersen, D.E., Mulder, F., Tyrring, T., Poulsen, T.B.
Structure (2020), 28, 528-539, PubMed 32220302 , DOI 10.1016/j.str.2020.03.003 , Abstract

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

3 3D HNCACB

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

4 3D HNCO

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

5 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

6 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

7 3D C(CO)NH

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

9 3D HN(CA)CO

Instrument

Bruker Avance - 500 MHz with a shielded-gradient TXI probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 3.25 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]		1-2 mM
2	potassium phosphate	natural abundance		10 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr50088_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr50088_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1107		100.0 (chain: 1, length: 93)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 93, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 619
  - ¹³C chemical shifts: 389
  - ¹⁵N chemical shifts: 99
- Completeness of assignments
  - Entity_assemble_ID: 1
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1